org.biopax.paxtools.io

Class BioPAXIOHandlerAdapter

java.lang.Object

org.biopax.paxtools.io.BioPAXIOHandlerAdapter

All Implemented Interfaces:

BioPAXIOHandler

Direct Known Subclasses:

SimpleIOHandler

public abstract class BioPAXIOHandlerAdapter
extends Object
implements BioPAXIOHandler

Field Summary

Fields

Modifier and Type	Field and Description
protected String	base
protected String	bp
protected EditorMap	editorMap
protected BioPAXFactory	factory
protected BioPAXLevel	level
protected Map<String,String>	namespaces
protected static String	owl
protected static String	rdf
protected static String	rdfs
protected static String	xsd

Constructor Summary

Constructors

Constructor and Description
BioPAXIOHandlerAdapter()
BioPAXIOHandlerAdapter(BioPAXFactory factory, BioPAXLevel level)
BioPAXIOHandlerAdapter(BioPAXLevel level)

Method Summary

Modifier and Type	Method and Description
protected void	bindValue(String valueString, PropertyEditor editor, BioPAXElement bpe, Model model) This method binds the value to the bpe.
Model	convertFromOWL(InputStream in) Reads a BioPAX model from an OWL file input stream (in) and converts it to a model.
void	convertToOWL(Model model, OutputStream outputStream, String... ids) Similar to BioPAXIOHandler.convertToOWL(org.biopax.paxtools.model.Model, java.io.OutputStream) (org.biopax.paxtools.model.Model, Object)}, but extracts a sub-model, converts it into BioPAX (OWL) format, and writes it into the outputStream.
protected void	createAndAdd(Model model, String id, String localName) This method is called by the reader for each OWL instance in the OWL model.
protected abstract void	createAndBind(Model model) This method provides a hook for the implementers of this abstract class to create objects themselves and bind the properties to the objects.
void	fixReusedPEPs(boolean fixReusedPEPs) Enables (true) or disables (false) the fixing of reused peps.
EditorMap	getEditorMap()
BioPAXFactory	getFactory()
BioPAXLevel	getLevel()
protected StringPropertyEditor	getRDFCommentEditor(BioPAXElement bpe) Paxtools maps BioPAX:comment (L3) and BioPAX:COMMENT (L2) to rdf:comment.
protected ReusedPEPHelper	getReusedPEPHelper() This is a helper class initialized only if fixReusedPEPs is true.
protected abstract void	init(InputStream in) This method provides a hook for the implementers of this abstract class to perform the initial reading from the input stream.
boolean	isFixReusedPEPs() Workaround for a very common Level 2 issue.
protected abstract Map<String,String>	readNameSpaces() This method provides a hook for the implementers of this abstract class to set the namespaces of the model.
protected void	reset(InputStream in)
protected abstract void	resetEditorMap() Updates the member EditorMap for the new BioPAX level and factory (different implementations of EditorMap can be used in modules, e.g.
protected void	resetLevel(BioPAXLevel level, BioPAXFactory factory) Updates the level and factory for this I/O (final - because used in the constructor)
protected Object	resourceFixes(BioPAXElement bpe, Object value) This method currently only fixes reusedPEPs if the option is set.
void	setEditorMap(EditorMap editorMap)
void	setFactory(BioPAXFactory factory)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.biopax.paxtools.io.BioPAXIOHandler

convertToOWL

Field Detail

level

protected BioPAXLevel level

factory

protected BioPAXFactory factory

editorMap

protected EditorMap editorMap

namespaces

protected Map<String,String> namespaces

rdf

protected static final String rdf

See Also:

Constant Field Values

rdfs

protected static final String rdfs

See Also:

Constant Field Values

bp

protected String bp

xsd

protected static final String xsd

See Also:

Constant Field Values

owl

protected static final String owl

See Also:

Constant Field Values

base

protected String base

Constructor Detail

BioPAXIOHandlerAdapter

public BioPAXIOHandlerAdapter()

BioPAXIOHandlerAdapter

public BioPAXIOHandlerAdapter(BioPAXLevel level)

BioPAXIOHandlerAdapter

public BioPAXIOHandlerAdapter(BioPAXFactory factory,
                              BioPAXLevel level)

Method Detail

resetLevel

protected final void resetLevel(BioPAXLevel level,
                                BioPAXFactory factory)

Updates the level and factory for this I/O (final - because used in the constructor)

Parameters:

level - BioPAX Level

factory - concrete BioPAX factory impl.

resetEditorMap

protected abstract void resetEditorMap()

Updates the member EditorMap for the new BioPAX level and factory (different implementations of EditorMap can be used in modules, e.g. SimpleEditorMap and JenaEditorMap.)

fixReusedPEPs

public void fixReusedPEPs(boolean fixReusedPEPs)

Enables (true) or disables (false) the fixing of reused peps.

Specified by:

fixReusedPEPs in interface BioPAXIOHandler

Parameters:

fixReusedPEPs - true if fixing is desired

See Also:

fixReusedPEPs

isFixReusedPEPs

public boolean isFixReusedPEPs()

Workaround for a very common Level 2 issue. Most level2 exports in the past reused PhysicalEntityParticipants as if they represent states. This is problematic because PEPs also contain stoichiometry information which is specific to a reaction. BioPAX spec says that PEPs should not be reused across reactions. As Level2 exports getting obsolete this method is slated for deprecation.

Specified by:

isFixReusedPEPs in interface BioPAXIOHandler

Returns:

true if this Handler automatically splits reused PEPs to interaction specific PEPS.

getReusedPEPHelper

protected ReusedPEPHelper getReusedPEPHelper()

This is a helper class initialized only if fixReusedPEPs is true.

Returns:

helper object

getFactory

public BioPAXFactory getFactory()

Specified by:

getFactory in interface BioPAXIOHandler

Returns:

the factory that is used to create new BioPAX POJOs during a BioPAXIOHandler operation.

setFactory

public void setFactory(BioPAXFactory factory)

Specified by:

setFactory in interface BioPAXIOHandler

Parameters:

factory - used for creating objects

getEditorMap

public EditorMap getEditorMap()

Specified by:

getEditorMap in interface BioPAXIOHandler

Returns:

EditorMap used for this handler.

setEditorMap

public void setEditorMap(EditorMap editorMap)

Specified by:

setEditorMap in interface BioPAXIOHandler

Parameters:

editorMap - used for this handler.

getLevel

public BioPAXLevel getLevel()

Specified by:

getLevel in interface BioPAXIOHandler

Returns:

The level of the model that is being read.

convertFromOWL

public Model convertFromOWL(InputStream in)

Reads a BioPAX model from an OWL file input stream (in) and converts it to a model.

Specified by:

convertFromOWL in interface BioPAXIOHandler

Parameters:

in - inputStream from which the model will be read

Returns:

an empty model in case of invalid input.

reset

protected void reset(InputStream in)

createAndAdd

protected void createAndAdd(Model model,
                            String id,
                            String localName)

This method is called by the reader for each OWL instance in the OWL model. It creates a POJO instance, with the given id and inserts it into the model. The inserted object is "clean" in the sense that its properties are not set yet. Implementers of this abstract class can override this method to inject code during object creation.

Parameters:

model - to be inserted

id - of the new object. The model should not contain another object with the same ID.

localName - of the class to be instantiated.

init

protected abstract void init(InputStream in)

This method provides a hook for the implementers of this abstract class to perform the initial reading from the input stream.

Parameters:

in - BioPAX RDF/XML input stream

readNameSpaces

protected abstract Map<String,String> readNameSpaces()

This method provides a hook for the implementers of this abstract class to set the namespaces of the model.

Returns:

a map of namespaces.

createAndBind

protected abstract void createAndBind(Model model)

This method provides a hook for the implementers of this abstract class to create objects themselves and bind the properties to the objects.

Parameters:

model - to be populated

resourceFixes

protected Object resourceFixes(BioPAXElement bpe,
                               Object value)

This method currently only fixes reusedPEPs if the option is set. As L2 is becoming obsolete this method will be slated for deprecation.

Parameters:

bpe - to be bound

value - to be assigned.

Returns:

a "fixed" value.

bindValue

protected void bindValue(String valueString,
                         PropertyEditor editor,
                         BioPAXElement bpe,
                         Model model)

This method binds the value to the bpe. Actual assignment is handled by the editor - but this method performs most of the workarounds and also error handling due to invalid parameters.

Parameters:

valueString - to be assigned

editor - that maps to the property

bpe - to be bound

model - to be populated.

getRDFCommentEditor

protected StringPropertyEditor getRDFCommentEditor(BioPAXElement bpe)

Paxtools maps BioPAX:comment (L3) and BioPAX:COMMENT (L2) to rdf:comment. This method handles that.

Parameters:

bpe - to be bound.

Returns:

a property editor responsible for editing comments.

convertToOWL

public void convertToOWL(Model model,
                         OutputStream outputStream,
                         String... ids)

Similar to BioPAXIOHandler.convertToOWL(org.biopax.paxtools.model.Model, java.io.OutputStream) (org.biopax.paxtools.model.Model, Object)}, but extracts a sub-model, converts it into BioPAX (OWL) format, and writes it into the outputStream. Saved data can be then read via BioPAXIOHandler interface (e.g., SimpleIOHandler).

Specified by:

convertToOWL in interface BioPAXIOHandler

Parameters:

model - model to be converted into OWL format

outputStream - output stream into which the output will be written

ids - optional list of "root" element absolute URIs; direct/indirect child objects are auto-exported as well.